Variant report

Variant	rs19801
Chromosome Location	chr22:34050561-34050562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13055437	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs240335	0.92[ASN][1000 genomes]
rs240336	0.84[ASN][1000 genomes]
rs240337	0.85[ASN][1000 genomes]
rs240338	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs240339	0.87[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs240340	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs240341	1.00[ASN][1000 genomes]
rs240342	0.87[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs240343	0.87[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs240344	0.87[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs240345	0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs240346	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs240347	0.87[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs240349	0.87[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs240350	0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs240351	0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs240352	0.88[ASN][1000 genomes]
rs240353	0.87[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs240354	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs240355	0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs240357	0.87[ASN][1000 genomes]
rs240358	0.83[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs240598	0.89[ASN][1000 genomes]
rs240600	1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs240601	1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs240602	0.86[ASN][1000 genomes]
rs240603	0.86[CHB][hapmap]
rs240604	0.87[CHB][hapmap]
rs240607	0.87[ASN][1000 genomes]
rs80215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9621748	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1062127	chr22:33755479-34085278	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544683	chr22:33755479-34085278	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv531588	chr22:33776857-34150188	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1055791	chr22:33822226-34159536	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1065417	chr22:33823850-34053325	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv933309	chr22:33825232-34053000	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv917167	chr22:33852676-34137036	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1062832	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv544686	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv914988	chr22:33975998-34083987	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv934161	chr22:33979015-34118621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv588935	chr22:34008430-34073758	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv914989	chr22:34011334-34083987	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs19801	NEFH	cis	parietal	SCAN
rs19801	DEPDC5	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33994200-34050600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:34003000-34062400	Weak transcription	Gastric	stomach
3	chr22:34019400-34050600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr22:34021400-34053000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr22:34036800-34055000	Weak transcription	Brain Anterior Caudate	brain
6	chr22:34040200-34056200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:34043000-34054800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr22:34043400-34050600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr22:34044400-34062200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr22:34045200-34053000	Weak transcription	Liver	Liver
11	chr22:34046200-34053400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr22:34046400-34053000	Weak transcription	Right Atrium	heart
13	chr22:34046400-34055000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr22:34046400-34055400	Weak transcription	Fetal Muscle Leg	muscle
15	chr22:34046600-34050600	Weak transcription	Colon Smooth Muscle	Colon
16	chr22:34046600-34052400	Weak transcription	Ovary	ovary
17	chr22:34046600-34053000	Weak transcription	Pancreas	Pancrea
18	chr22:34046600-34056200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr22:34046600-34056400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr22:34046600-34059400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr22:34046800-34050600	Weak transcription	Adipose Nuclei	Adipose
22	chr22:34046800-34053000	Weak transcription	Right Ventricle	heart
23	chr22:34046800-34053000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr22:34046800-34053200	Weak transcription	Fetal Stomach	stomach
25	chr22:34046800-34062200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr22:34048000-34054800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr22:34048200-34050600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr22:34048200-34050600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr22:34048400-34050800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr22:34048400-34051000	Enhancers	Fetal Intestine Small	intestine
31	chr22:34048400-34051200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr22:34048800-34051000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr22:34049000-34051000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr22:34049000-34055000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr22:34049400-34050600	Weak transcription	Fetal Heart	heart
36	chr22:34049400-34052600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr22:34049600-34050600	Enhancers	Psoas Muscle	Psoas
38	chr22:34049600-34050800	Enhancers	Left Ventricle	heart
39	chr22:34049600-34051000	Enhancers	Fetal Intestine Large	intestine
40	chr22:34049800-34050600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr22:34049800-34050800	Enhancers	Lung	lung
42	chr22:34049800-34051000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr22:34049800-34051200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr22:34049800-34051600	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr22:34049800-34052200	Weak transcription	Stomach Mucosa	stomach
46	chr22:34050200-34050600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr22:34050200-34050800	Enhancers	Small Intestine	intestine
48	chr22:34050200-34051600	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr22:34050200-34062200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr22:34050400-34050600	Enhancers	Brain Germinal Matrix	brain

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